I had the same problem (E6, clunking, etc...), for the life of me couldn't figure it out. rewound my bobbin tons of times. finally walked away.
Came back to it the next day and it was the stupidest thing ever. The thread was miswound inside the machine - not down by the bobbin but up top. So, I undid the top thread and rethread it through the machine and all was fine. has been fine since.